Energy study at different solvents for potassium Channel Protein by Monte Carlo, Molecular and Langevin Dynamics Simulations
محورهای موضوعی : Journal of Physical & Theoretical ChemistryF. Mollaamin 1 , T. Nejadsattari 2 , I. Layali 3
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کلید واژه: Nanomolecular simulation, Channel Protein, Gyration Radius, Protein folding, Monte Carlo, Molecular Dynamics, Langevin Dynamics simulation,
چکیده مقاله :
Potassium Channels allow potassium flux and are essential for the generation of electric current acrossexcitable membranes. Potassium Channels are also the targets of various intracellular controlmechanisms; such that the suboptimal regulation of channel function might be related to pathologicalconditions. Realistic studies of ion current in biologic channels present a major challenge for computersimulation approaches. Molecular dynamics simulations may be used to probe the interactions ofmembrane proteins with lipids and with detergents at atomic resolution .Examples of such simulationsfor ion channels and for bacterial outer membrane has already been studied. In this work, to characterizeprotein behavior, we observed quantities such as gyration radius and energy average. It was studied thechanges of these factors for potassium channel Protein in gas, water, Methanol and Ethanol phases withnative conformation by Monte Carlo, Molecular and Langevin Dynamics simulations. Monte Carlosimulation is stochastic method and therefore, is the best method to evaluate the radius of gyration in gasphase. when the temperature is increased the kinetic energy is increased too, and its correlation is linear.All the calculations were carried out By Hyperchem 8.0 program. The radius of gyration for differentsolvent is calculated by VMD 1.8.7 Software. The determination of gyration radius is a spectacular forconfiguration of a Macromolecule. It also reflects molecular compactness shape. Monte Carlo simulationis the best method to evaluate gyration radius.
